Posts load differently depending on permalink structure.

I have my site running how I would like it, except when I simply change the permalink structure.

I removed all archive templates and every post now loads directly in index, but for some reason the permalink structure still affects how the page loads and I cannot figure out how to adjust it. For example, with the permalinks set to only date, when you click on the orange arrows to the right or left of the content (next and previous) the calendar widget automatically adjusts to show the current post date you are viewing, even when moving to a new month.

When I change the permalink to /%postname%/, the calendar stops working from month to month, the social link buttons under the content disappear, and the default WP like and sharing buttons appear.

Any suggestions?

http://www.thejunglecomic.com/